Test planes

[aneshps]

Is it possible to add test planes to record the (position, time of arrival, temperature, kinetic energy) at different locations, just like testplane.lua in simion? That would be helpful to figure out exactly where the resolution loss happens in the device by plotting the arrival time distributions at different locations.

Thank you
Aneesh

[wwissdorf]

It is planned to implement such a feature as one of the next development steps. However, it will probably take some weeks to do so due to general workload.

[aneshps]

I tried the following script and it seems working reasonably well for me. This script extract the values closes to a plane, from the trajectory file.

import numpy as np
import IDSimPy as idpy

# Load trajectory data
tra = idpy.read_hdf5_trajectory_file("trajectories.h5")

# Chemical ID to Mass mapping
mass_mapping = {0: 322, 1: 622, 2: 922, 3: 1222, 4: 1522}   #map mass (m/z) values to the chemical ids. This is to replace the chemical ids with corresponding mass, just for convenience.

# Parameters
z_target = 0.204  # Target z position in meters
delta_z = 0.0003   # Tolerance for z position just give a tolerance to find data closest to the defined plane

# Get time array
times = tra.times
n_timesteps = len(times)

# Storage for results
arrival_times = []
arrival_masses = []

# Iterate over all timesteps
for t_index in range(n_timesteps):
    # Get positions at this timestep
    p_pos = tra.get_positions(t_index)  # Positions of particles
    z_pos = p_pos[:, 2]  # Z-coordinates

    # Find particles within the z_target ± delta_z range
    valid_indices = np.where((z_pos >= z_target - delta_z) & (z_pos <= z_target + delta_z))[0]

    # If valid indices exist, record their data
    if len(valid_indices) > 0:
        valid_times = [times[t_index]] * len(valid_indices)
        valid_chemical_ids = tra.particle_attributes.get("chemical id")[valid_indices, t_index]
        valid_masses = [mass_mapping[chemical_id] for chemical_id in valid_chemical_ids]

        # Append to result lists
        arrival_times.extend(valid_times)
        arrival_masses.extend(valid_masses)

# Output to file
output_file = "ToA_plane.dat"
with open(output_file, "w") as f:
    # Write header
    f.write("# Z Target Data\n")
    f.write(f"# Target Z-Position: {z_target}\n")
    f.write(f"# Tolerance (delta Z): {delta_z}\n")
    f.write("# Time Mass\n")
    for time, mass in zip(arrival_times, arrival_masses):
        f.write(f"{time:.6f} {mass}\n")

print(f"Data saved to {output_file}")

[wwissdorf]

@aneshps Is the feature still required or are you good with your script?